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- PDB-5xmf: Crystal structure of feline MHC class I for 2,1 angstrom -

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Basic information

Entry
Database: PDB / ID: 5xmf
TitleCrystal structure of feline MHC class I for 2,1 angstrom
Components
  • Beta-2-microglobulin
  • Gag polyprotein
  • MHC class I antigen alpha chain
KeywordsIMMUNE SYSTEM / domestic cats / MHC I / Feline immunodeficiency virus / CTL immunity
Function / homology
Function and homology information


viral budding via host ESCRT complex / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding ...viral budding via host ESCRT complex / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / viral nucleocapsid / structural constituent of virion / nucleic acid binding / immune response / lysosomal membrane / extracellular region / zinc ion binding
Similarity search - Function
: / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like ...: / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / : / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / Gag polyprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesFelis catus (domestic cat)
Feline immunodeficiency virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiang, R. / Sun, Y. / Wang, J. / Wu, Y. / Zhang, N. / Xia, C.
Funding support China, 3items
OrganizationGrant numberCountry
the 973 Project of the China Ministry of Science and TechnologyNO.2013CB835302 China
state key program of the National Natural Science Foundation of ChinaNO. 31201887 China
the 863 Project of the China Ministry of Science and TechnologyNO. 2013AA102503 China
CitationJournal: J. Virol. / Year: 2018
Title: Major Histocompatibility Complex Class I (FLA-E*01801) Molecular Structure in Domestic Cats Demonstrates Species-Specific Characteristics in Presenting Viral Antigen Peptides
Authors: Liang, R. / Sun, Y. / Liu, Y. / Wang, J. / Wu, Y. / Li, Z. / Ma, L. / Zhang, N. / Zhang, L. / Wei, X. / Qu, Z. / Zhang, N. / Xia, C.
History
DepositionMay 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen alpha chain
B: Beta-2-microglobulin
C: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)44,5583
Polymers44,5583
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, one MHC I heavy chain, one B-microglobulin and one peptide
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-13 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.421, 83.379, 121.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen alpha chain


Mass: 31947.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: FLA-I / Production host: Escherichia coli (E. coli) / References: UniProt: C6ZK72
#2: Protein Beta-2-microglobulin


Mass: 11618.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q5MGS7
#3: Protein/peptide Gag polyprotein


Mass: 993.143 Da / Num. of mol.: 1 / Fragment: UNP residues 40-48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus / Strain: isolate Petaluma / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: P16087
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: PEG/Ion solution No. 23 (0.2M ammonium formate and 20%(w/v) polyethylene glycol 3,350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 27016 / % possible obs: 99.55 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.542 / Rsym value: 0.063 / Net I/σ(I): 7.31
Reflection shellResolution: 2.103→2.157 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 30.971 / Rsym value: 0.063 / % possible all: 99.55

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PWV

3pwv


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.797 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25521 1404 4.9 %RANDOM
Rwork0.2133 ---
obs0.21533 27016 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.479 Å2
Baniso -1Baniso -2Baniso -3
1--3.24 Å20 Å2-0 Å2
2--0.53 Å20 Å2
3---2.71 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 0 211 3346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193220
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.9274372
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2965380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47923.39177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44815525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6821532
X-RAY DIFFRACTIONr_chiral_restr0.0670.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212534
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.332.7391529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6344.0971906
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7283.0551691
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined2.84123.8285001
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.04433220
X-RAY DIFFRACTIONr_sphericity_free27.6581
X-RAY DIFFRACTIONr_sphericity_bonded11.65953265
LS refinement shellResolution: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 126 -
Rwork0.257 1946 -
obs--98.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.12780.0947-0.0220.2788-0.02180.0090.0284-0.02260.00220.0523-0.03130.00360.00680.01730.00280.1303-0.00230.00050.0651-0.0010.002924.87254.432117.6692
20.70740.3010.1910.19990.06160.0575-0.01570.05330.0573-0.01850.00390.03470.00050.02360.01180.131-0.0111-0.00850.0431-0.00790.013315.573512.0728
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 276
2X-RAY DIFFRACTION2B1 - 99

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